Rhizomania ebook free download

Enrico Biancardi · Tetsuo Tamada
Editors

Rhizomania


Rhizomania



Enrico Biancardi • Tetsuo Tamada
Editors

Rhizomania


Editors
Enrico Biancardi
Stazione Sperimentale di Bieticoltura
Rovigo, Italy

Tetsuo Tamada
Agricultural Research Institute
Hokuren Federation of Agricultural
Cooperatives
Naganuma, Hokkaido, Japan

ISBN 978-3-319-30676-6
ISBN 978-3-319-30678-0
DOI 10.1007/978-3-319-30678-0

(eBook)

Library of Congress Control Number: 2016946022
© Springer International Publishing Switzerland 2016
Chapter 9 was created within the capacity of an US governmental employment. US copyright protection
does not apply.
This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of
the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation,
broadcasting, reproduction on microfilms or in any other physical way, and transmission or information
storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology
now known or hereafter developed.
The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication
does not imply, even in the absence of a specific statement, that such names are exempt from the relevant
protective laws and regulations and therefore free for general use.
The publisher, the authors and the editors are safe to assume that the advice and information in this book
are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the
editors give a warranty, express or implied, with respect to the material contained herein or for any errors
or omissions that may have been made.
Printed on acid-free paper
This Springer imprint is published by Springer Nature
The registered company is Springer International Publishing AG Switzerland


“To my wife Donatella, who accepted to
spend her life not only with me but also with
the genus Beta”
—Enrico Biancardi
“To my wife Sachiko and my daughters
Machiko and Chieko who gave warm support
to my BNYVV work”

—Tetsuo Tamada



Foreword

An unknown disease of sugar beet was detected in Italy more than 50 years ago.
Soon the new syndrome displayed devastating effects on yield. This greatly concerned the Italian sugar beet growers and processors, especially considering that the
syndrome had spread to the most important Italian cultivation areas.
It was the start of a memorable enterprise for pathologists, breeders, and agronomists. The spontaneous and unusual synergy created among the universities,
research stations, seed companies, and grower associations led not only at the first
very appropriate attempts of prophylaxis measures but also to an awareness that the
only possible management would be through the use of resistant varieties. In this
phase, the Beta maritima germplasm selected at Rovigo and later at Salinas began
to display its value against the new disease called “rizomania.” Some resistant varieties were released, thanks to enhanced knowledge of the pathogenic agents (beet
necrotic yellow vein virus and Polymyxa betae) obtained in Japan and Germany.
It also was the beginning of countless research projects and collaborations worldwide, which, in a relatively short time, led to almost complete control of the disease.
There are perhaps few other diseases, even affecting more important crops, on
which so many papers have been published. It should be noted that the most significant results in the discovery of rhizomania resistance traits were obtained by public
research stations, often without any specific funding.
The future of sugar beet currently is endangered by the development of resistant
strains in the virus, among other things. I believe that it also will be possible to
overcome these new obstacles with the help of the powerful tools provided by
molecular investigation and following the knowledge carefully collected in this very
useful book, the first devoted exclusively to rhizomania.
The issue was much more difficult 50 years ago, when no one knew anything
about the syndrome and the researchers only had their eyes to see, a microscope to
look closer, and a pencil to take notes.
Alma Mater Studiorum
Bologna, Italy

May 2016

Antonio Canova

vii



Preface

This book is the result of an international enterprise among researchers involved in
past and present studies on rhizomania, a relatively new and devastating disease of
sugar beet. In less than 50 years, the disease has become the most damaging biotic
factor affecting the crop worldwide. Moreover, its spread is still ongoing in every
cultivated area. Because the traditional management systems were almost ineffective, it was soon evident that the employment of genetic resistances was the only
chance for limiting the economic damage. The discovery of the pathogenic agents
and the release of the first resistant varieties are described by some of the researchers directly involved.
The breeding efforts led to both the current satisfactory management of the disease and to the survival of the beet sugar industry in several areas. The cooperation
between the Italian and American Experimental Stations, born spontaneously about
80 years ago and still continuing today, should be remembered. The friendly collaboration led to the employment of genetic traits extracted from Beta maritima,
which became the sole source so far of the resistances available against the
disease.
The introduction briefly describes sugar beet cultivation, the more common diseases, and the damage caused by rhizomania. This is necessary because the book
also is addressed to readers who are not directly involved with sugar beet. Without
these brief explanations, some parts of the text would not be fully comprehensible.
The following chapters refer to the molecular physiology of the disease agents and
their interactions with the environment and the host-plant. The knowledge of ecology and epidemiology of rhizomania is, above all else, necessary to understand the
means and practices valuable to avoid or at least delay the further spread of the
disease into healthy soils. Some promising methods of control using concurrent but
not damaging viruses, bacteria, and fungi are in progress. They could help the action

of the genetic resistances, which are not completely effective. The integrated protection is useful, especially in the even more frequent occurrences of resistancebreaking strains of BNYVV, where the known types of resistance seem to have
partially lost their original efficacy. Some almost immune transgenic varieties are
already awaiting release. For traditional breeding, further efforts will be needed in
ix


x

Preface

search of new resistances in the wild species of the genus Beta. The availability of
large collections of Beta germplasm collected all over the world should ensure further success in this direction. The target will be gained by means of conventional
selection methods, assisted by updated techniques for genome analyses. Finally,
perspectives are described to not only reduce the current damages but also to avoid
further spread and noxious evolutions of rhizomania agents.
By means of interdisciplinary approaches, this book was edited above all to provide a broad, comprehensive, and updated overview of the various aspects of rhizomania, now scattered in countless publications. The outlook should be valuable for
farmers, extension services, students, and researchers committed to ensuring the
future of the sugar beet crop.
Rovigo, Italy
Naganuma, Japan

Enrico Biancardi
Tetsuo Tamada


Acknowledgments

Antonio Canova must be recognized for his encouragement and convincing and
enthusiastic support of this enterprise. The editors are grateful to Bob Lewellen, Lee
Panella, and Mitch McGrath for their contributions and critical reading and revisions of the text and proofs. Special thanks go to Piergiorgio Stevanato for his help

in translating and organizing the manuscript. Together with Mauro Colombo, he
collaborated on the digital drawing of tables and figures. Many thanks are also
addressed to Kelley Richardson for editing Chap. 12. Loving thanks are given by
Biancardi to his wife for the original watercolor printed in the first pages of the
book. Tamada is grateful to his colleague Hideki Kondo for generous help with
tables and figures in parts of this book. His long-term research on rhizomania was
carried out at Hokkaido Central Agricultural Experiment Station and Institute of
Plant Science and Resources, Okayama University, and financially supported by
Hokkaido Sugar Beet Associations.
The editors express also their gratitude to the numerous colleagues for the confidence given when the prospects for this book were still in the early stages of discussion and development. Finally, grateful memory must be addressed to the
Italian researchers who firstly contributed both to the discovery of the disease agents
and to plant-host resistance, which allowed survival and development of the sugar
beet crop and the connected sugar industry.

xi



Contents

Part I

Historical Background

1

Introduction .............................................................................................
Enrico Biancardi and Robert T. Lewellen

3

2

History and Current Status....................................................................
Antonio Canova, Luciano Giunchedi, and Enrico Biancardi

29

Part II The Virus
3

General Features of Beet Necrotic Yellow Vein Virus ..........................
Tetsuo Tamada

4

Molecular Biology and Replication of Beet Necrotic
Yellow Vein Virus.....................................................................................
David Gilmer

5

55

85

Genetic Diversity of Beet Necrotic Yellow Vein Virus .......................... 109
Tetsuo Tamada, Hideki Kondo, and Sotaro Chiba

Part III The Vector

6

The Plasmodiophorid Protist Polymyxa betae ...................................... 135
Tetsuo Tamada and Michael Asher

7

Ecology and Epidemiology ..................................................................... 155
Tetsuo Tamada and Michael Asher

Part IV

Control and Resistance Breeding

8

Control of the Disease ............................................................................. 175
Claudio Ratti and Enrico Biancardi

9

Genetic Resistances ................................................................................. 195
Leonard W. Panella and Enrico Biancardi
xiii


xiv

Contents

10

Engineering Transgenic Rhizomania Resistance ................................. 221
Ourania I. Pavli and George N. Skaracis

11

Breeding Methods ................................................................................... 233
Marco De Biaggi and Enrico Biancardi

12

Assisted Selection .................................................................................... 249
Piergiorgio Stevanato, Enrico Biancardi, and Peyman Norouzi

13

Perspective ............................................................................................... 263
J. Mitchell McGrath

Appendix .......................................................................................................... 271
Index of Names ................................................................................................ 273


Author’s Contributions to Rhizomania Research

Michael J.C. Asher Studied the ecology and epidemiology of Polymyxa betae and
sources of resistance in wild Beta species, identifying two genes carrying the trait.
Contributed to models predicting the development and spread of rhizomania and to
the development of molecular markers for novel sources of resistance.

Enrico Biancardi Classified as “Alba type” the multigenic rhizomania resistance
carried by old Italian genotypes. Collected sea beet populations in the Po River
Delta, from which new sources of resistance were identified and developed. Lead
author and editor in books, reviews, papers on aspects of research on rhizomania
and Beta maritima.
Antonio Canova In 1966, hypothesized the connection “virus A”-Polymyxa betae
as cause of the “low sugar content syndrome”. Polymyxa betae, identified and classified a few years before by Keskin, plays the role of carrier, while the real pathogen
is the virus. He named the disease “rizomania”, later anglicized to rhizomania.
Sotaro Chiba Collaborated with Tamada and identified amino acids of the p25
protein for induction of the resistance response in leaves of Beta vulgaris and found
function of the p25 protein as an avirulence factor. He analyzed worldwide isolates
of BNYVV and obtained information on the global biogeography, evolution, virulence, and spread of BNYVV.
Marco De Biaggi In 1978, together with Biancardi, discovered and selected rhizomania resistance traits in cercospora leaf spot resistant genotypes. In 1985, released
the first monogenic resistant variety endowed with the “Rizor type” resistance. He
was among the first to apply ELISA techniques in screening beets for mass selection. In collaboration with Stevanato and Biancardi, he recently verified the similarity between the resistances Rizor and Holly (Rz1).
David Gilmer Studies molecular biology of BNYVV looking for RNA and protein
structure-function relationships. Aims to understand BNYVV viral cycle.
xv


xvi

Author’s Contributions to Rhizomania Research

Luciano Giunchedi Collaborated with Canova on the etiology of rhizomania, and
later with De Biaggi in characterizing the mechanisms of the Rizor resistance in
reducing the damages caused by BNYVV.
Hideki Kondo Collaborated with Tamada since 1995. He studied with Andika the
molecular mechanisms of RNA silencing in roots and root-specific suppression of
RNA silencing. He analyzed genetic diversity of BNYVV and evolution of benyviruses, and discovered benyvirus replicase-related sequences integrated into the

genomes of diverse eukaryotic organisms.
Robert T. Lewellen Determined inheritance and named the gene Rz (the “Holly
type” resistance) after discovery by Erichsen and his subsequent release of the variety “Rhizosen” in 1990. Resistance to BNYVV was found in Beta maritima accessions collected in Europe. Released lines, as C48, C79, and R740, were used
internationally to identify Rz2, Rz3, Rz4, and Rz5 and incorporated into commercial resistant varieties. With Wisler devised disease severity scale and its correlation
with concentration of BNYVV. More recently, with Liu, discovered evidence of
resistance-breaking strains of BNYVV and used Beta macrocarpa as systemic host
to incorporate specific virus strains with Polymyxa betae. With Biancardi and
Panella, published extensively on rhizomania research and resistance, particularly
from Beta maritima.
J. Mitchell McGrath Has a long-standing interest in the genetics, genomics, and
germplasm enhancement of sugar beets. He actively releases sugar beet germplasm
with novel genetic characters and investigates the organization of the beet genome.
Resistance gene structure and function, including rhizomania genes, is a recent
interest afforded by a complete genome sequence.
Peyman Norouzi Identified some molecular markers linked to rhizomania resistance genes and selected many pollinators, OType lines, and populations accordingly. He co-authored papers published by Stevanato regarding the identification of
SNP markers linked to rhizomania resistance genes. He collaborated to develop
transgenic lines resistant to rhizomania and other traits.
Leonard W. Panella In collaboration, with Biancardi and Lewellen, co-authored
the book “Beta maritima: the origin of beets”. Collected seed of Beta maritima and
other wild beets, including Beta nana and Beta patellaris (Patellifolia patellaris), in
many parts of the world. In collaboration with Stevanato and colleagues, developed
molecular genetic markers for resistance to BNYVV. Developed enhanced germplasm that combined resistances to rhizomania, cercospora leaf spot, and rhizoctonia root rot.
Claudio Ratti Studied the epidemiology of BNYVV in Italy and in Europe developing molecular methods for detection and characterization of BNYVV types.
Together with Gilmer, currently studies the biology of members of family


Author’s Contributions to Rhizomania Research

xvii

Benyviridae by reverse genetic approach with particular attention to BNYVV and
beet soil-borne mosaic virus (BSBMV).
George N. Skaracis and Ourania I. Pavli Authored several publications regarding
conventional and molecular breeding methods, with emphasis on genetic engineering, to develop durable rhizomania resistance.
Piergiorgio Stevanato Collected seed of sea beet populations in the countries bordering the Adriatic Sea. Authored several publications together with Panella,
Lewellen, Biancardi, De Biaggi, Pavli, and Skaracis. Improved the molecular methods for identifying and more rapidly increase the resistances to rhizomania, bolting,
fusarium yellows, and Heterodera schachtii.
Tetsuo Tamada Identified the causal agent of rhizomania and named it “beet
necrotic yellow vein virus” (BNYVV) in 1973. Since then, he worked with many
colleagues on the characterization of virus, vector transmission, detection and diagnosis, ecology, and control. In 1995, he moved to Institute of Plant Science and
Resources of Okayama University and continued to work on biological and molecular properties of BNYVV. Identified viral genes involved in vector transmission,
disease development, and genetic resistances. Published extensively on the results.



Abbreviations

2x, 3x, 4x (or 2n, 3n, 4n)
A
aa
AD
AGO
AK
AMOVA
ANB
ARS
ASSBT
Avr
BaYMV
Bb

BBSV
BCTV
BdMoV
BMYV
BNYVV
BOLV
BRLS
BSBMV
BSBV
BSMV
BVQ
°Bx
BWYV
BYV
C
Cas9
CAV
CC

Diploid, triploid, tetraploid genotypes
Alanine
Amino acids
Activation domain
Agronatute
Alkalinity coefficient
Analysis of molecular variance
Italian Sugar Beet Growers Association
Agricultural Research Service
American Society of Sugar Beet Technologists
Avirulence

Barley yellow mosaic virus
Annuality (alleles)
Beet black scorch virus
Beet curly top virus
Burdock mottle virus
Beet mild yellowing virus
Beet necrotic yellow vein virus
Beet oak leaf virus
Benyvirus replicase-related sequence
Beet soil-borne mosaic virus
Beet soil-borne virus
Barley stripe mosaic virus
Beet virus Q
Brix (refractometer degree or optical density)
Beet western yellows virus
Beet yellows virus
Cysteine
CRISPR-associated protein 9
Chara australis virus
Coiled-coil
xix


xx

CCC
cDNA
CdTe
CEC
CHS

CLS
cM
CMS
CP

CRA-CIN
CRISPR
CRP
CWR
D
DAS-ELISA
DCL
D-D
DI
dN
DNA
DPI
dS
dsRNA
dT
E
E, N, Z
ed, eds
EDTA
eGFP
ELISA
EPPO
ER
F
F-box

FLIM
FRET
GFP
GM
GMO
GO

Abbreviations

Copyright Clearance Center (www.copyright.com)
Complementary DNA
Cadmium telluride
Cation exchange capacity
Chalcone synthase
Cercospora leaf spot
Centimorgan
Cytoplasmic male sterility
Coat protein or capsid protein
Cross-protection test
CP-mediated protection
Centro per la Ricerca in Agricoltura – Centro per le
Colture Industriali
Clustered regularly interspaced short palindromic
repeats
Cysteine-rich protein
Crop wild relatives
Aspartic acid
Double-antibody sandwich enzyme-linked immunosorbent assay
Dicer-like
Mixture dichloropropene + dichloropropane

Disease index
Non-synonymous substitution
Deoxyribonucleic acid
Days post inoculation
Synonymous substitution
Double-stranded RNA
Deoxythymidine
Glutamic acid
Production ability of sugar beet varieties
Editor, editors
Ethylenediaminetetraacetic acid
Enhanced green fluorescent protein
Enzyme-linked immunosorbent assay
European-Mediterranean Plant Protection Organization
Endoplasmic reticulum
Phenylalanine
Cyclin F motif-containing protein
Fluorescence lifetime imaging
Fluorescence resonance energy transfer
Green fluorescent protein
Genetically modified
Genetically modified organism
Argonaute


Abbreviations

GORV
Gp-1a, GP1b, GP-2, GP-3
GSP

GST
H
Hel
HR
HrpZ
Ibid.
IBPGR
IIRB
IMP
ISEM
ITS
IWGPVFV
kDa
kPa
KWS
L
LAI
LSCS
LSD
MAPK
ML
Mm
mM
MP
MPN
mRFP
mRNA
MS
MT
N

NB-LRR
NCR
ncRNA
NES
NGS
NLS
NoLS
nPCR
nt
NTPase
NVMV

xxi

Gentian ovary ring-spot virus
Primary, secondary, and tertiary Beta gene pool
Gene-specific primer
Glutathione S-transferase
Histidine
Helicase
Hypersensitive response
Harpin Z
Published in the formerly cited paper
International Board Plant Genetic Resources
International Institute of Sugar Beet Research
Immunodominant membrane protein
Immunosorbent electron microscopy
Internal transcribed spacers
International Working Group on Plant Viruses with
Fungal Vectors

Kilodalton
Kilopascal
Kleinwanzlebener Saatzucht (seed company)
Leucine
Leaf area index
Low sugar content syndrome
Least significant difference
Mitogen-activated protein kinase
Maximum likelihood
Monogermity (alleles)
Millimoles
Movement protein
Most probable number
Monomeric red fluorescent protein
Messenger RNA
Male sterility
Methyltransferase
Normal cytoplasm
Nucleotide-binding site-leucine-rich repeat
Noncoding region
Noncoding RNA
Nuclear exporting signal
Next-generation sequencing
Nuclear localization signal
Nucleolar localization signal
Nested PCR
Nucleotides
Nucleoside triphosphatase
Nicotiana velutina mosaic virus

xxii

OA
ORF
O-Type
p, pp
PCR
PCV
Pd
PDR
pH
PMTV
ppm
PR
Pro
Psph
PTGS
PVX
QD
qPCR
qRT-PCR
QTL
RB
RdDM
rDNA
RdRp
Rep0/3/5/III
RFLP
RISC

RNA
RNAi
ROS
rpm
rRNA
RS
RSNV
RT
RTD
RT-PCR
Rz1; Rz2; Rz3; Rz4; Rz5
Rz1rz1; Rz2rz2; Rz3rz3 etc.
S
°S
SBWMV
scFv
SDS

Abbreviations

Origin of assembly
Open reading frame
CMS maintainer
Page, pages
Polymerase chain reaction
Peanut clump virus
Plasmodesmata
Pathogen-derived resistance
Acidity/basicity of aqueous solution
Potato mop-top virus

Parts per million
Pathogenesis-related
Protease
Pseudomonas syringae pv. phaseolicola
Posttranscriptional gene silencing
Potato virus X
Quantum dot
Quantitative polymerase chain reaction
Quantitative reverse transcriptase polymerase chain
reaction
Quantitative trait locus
Resistance-breaking
RNA-directed DNA methylation
Ribosomal DNA
RNA-dependent RNA polymerase
Replicon 0, 3, 5 or III
Restriction fragment length polymorphism
RNA-induced silencing complex
Ribonucleic acid
RNA interference
Reactive oxygen specie
Revolutions per minute
Ribosomal RNA
Rizomania Signal (in German)
Rice stripe necrosis virus
Read-through
Read-through domain
Reverse transcriptase polymerase chain reaction
Resistances to rhizomania
Alleles of rhizomania resistances

Sterile cytoplasm
Polarization or sugar content (% w/w)
Soil-borne wheat mosaic virus
Single-chain antibody fragment
Sodium dodecyl sulfate


Abbreviations

SES
siRNA
SNP
SP
sp.
spp.
SSCP
ssRNA
subsp.
T
TA
TAS-ELISA
TEM
TEV
TGB
TIR
TMV
TRV
USDA
UTR
V

VIGS
VLRA
VSR
VY
w/v
w/w
WB
WSSMV
XRN
XxZz
μl

xxiii

Societè Europeenne des Semences (seed company)
Small interfering RNA
Single-nucleotide polymorphism
Signal peptide
Species (singular)
Species (plural)
Single-strand conformation polymorphism
Single-stranded RNA
Subspecies
Tyrosine
Transcriptional activation
Triple-antibody sandwich enzyme-linked immunosorbent assay
Transmission electron microscopy
Tobacco etch virus
Triple gene block
Toll/interleukin-1 receptor

Tobacco mosaic virus
Tobacco rattle virus
US Department of Agriculture
Untranslated region
Valine
Virus-induced gene silencing
Virus-like RNA assembly
Viral suppressor of RNA silencing
Virus yellows
Weight unit of solute in volume units of solution
Weight units of solute in weight units of solution
Wild beet
Wheat spindle streak mosaic virus
Exoribonuclease
Male sterility (alleles)
Microliters